Table 4 Databases and their access policies considered for the requirement clusters of data bridges

Requirement cluster: Imaging bridge

See: Additional file 1: Table S1

Mouse tissue imaging data (Infrafrontier), Human tumour tissue data (BBMRI/ FIMM), MitoCheck (cell-based RNAi screens), WebMicroscope (mouse and human image data sets), Ensembl, ArrayExpress, Phenotator, MitoCheck

Restricted access, data linking only possible, if the data provider gives permission based on the availability of informed consents, consent form which permits such a research may be required, application to the steering committee or principal investigator, Images are owned by image generator

Requirement cluster: Phenotypic bridge

See: Additional file 1: Table S2

EuroPhenome, IMPC, Gene Expression Atlas (GXA), ArrayExpress, ChEMBL, Metabolights, Reactome, CERM datasets, Biobank/BBMRI (University of Graz, Austria)

Predominantly open access, open restricted for private data (pre-publication/ unpublished), open access, when data is used for research purposes, biobank with restricted access (access rules include project application and approval committee)

Requirement cluster: Personalised Medicine bridge

See: Additional file 1: Table S3

ICGC (International Cancer Genome Consortium), TCGA (The Cancer Genome Atlas), EGA (European Genome-phenome Archive), Cosmic (Catalogue of somatic mutations in cancer), GEO (Gene Expression Omnibus), Array-Express, ChEMBL, Reactome, Ensembl, Drugbank, Pharmgkb, BioSD, Biobanks (BBMRI), EU-OPENSCREEN, ECRIN (CTIM), FIMM Institute for Molecular Medicine Finland (EATRIS)

Open access and data with and without restricted access, different policies apply, controlled access datasets means access control, Data Access Compliance Office (DACO) handles requests from scientists for access to controlled data, requirement for user certification via Data Access Request, download of datasets must be approved by the specified Data Access Committee (DAC), requires users to sign a Data Access Agreement (DAA), which details the terms and conditions of use for each dataset, all controlled access downloadable datasets are encrypted, restricted access usually for pre-published/unpublished data

Requirement cluster: Structural Data bridge

See: Additional file 1: Table S4

UniProt, AmiGO (Gene Ontology database), EMDB (Electron Microscopy Data Bank), IntAct (Molecular Interaction Database), GenBank (NCBI), ELIXIR, BMB database

All are open access

Requirement cluster: Biosample data bridge

See: Additional file 1: Table S5

Mainly restricted access. Open access for aggregated anonymised information or metadata about samples, for data access researcher has to apply to Data Access Committee (DAC) of biobank and has to agree to use data only for research, which has been specified between biobank and researcher, and not to try to identify patients